view mayachemtools/docs/modules/txt/TopologicalAtomTorsionsFingerprints.txt @ 5:9a001a14a022 draft

Deleted selected files

NAME
    TopologicalAtomTorsionsFingerprints

SYNOPSIS
    use Fingerprints::TopologicalAtomTorsionsFingerprints;

    use Fingerprints::TopologicalAtomTorsionsFingerprints qw(:all);

DESCRIPTION
    TopologicalAtomTorsionsFingerprints class provides the following
    methods:

    new, GenerateFingerprints, GetAtomTorsionsIDs, GetDescription,
    SetAtomIdentifierType, SetAtomicInvariantsToUse,
    SetFunctionalClassesToUse, StringifyTopologicalAtomTorsionsFingerprints

    TopologicalAtomTorsionsFingerprints is derived from Fingerprints class
    which in turn is derived from ObjectProperty base class that provides
    methods not explicitly defined in TopologicalAtomTorsionsFingerprints,
    Fingerprints or ObjectProperty classes using Perl's AUTOLOAD
    functionality. These methods are generated on-the-fly for a specified
    object property:

        Set<PropertyName>(<PropertyValue>);
        $PropertyValue = Get<PropertyName>();
        Delete<PropertyName>();

    The current release of MayaChemTools supports generation of
    TopologicalAtomTorsionsFingerprints corresponding to following
    AtomtomIdentifierTypes:

        AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
        FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
        SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes

    Based on the values specified for AtomIdentifierType along with other
    specified parameters such as AtomicInvariantsToUse and
    FunctionalClassesToUse, initial atom types are assigned to all
    non-hydrogen in a molecule. All unique atom torsions are identified and
    an atom torsion identifier is generated; the format of atom torsion
    identifier is:

        <AtomType1>-<AtomType2>-<AtomType3>-<AtomType4>

        AtomType1, AtomType2, AtomType3, AtomTyp4: Assigned atom types

        where AtomType1 <= AtomType2 <= AtomType3 <= AtomType4

    The atom torsion identifiers for all unique atom torsions corresponding
    to non-hydrogen atoms constitute topological atom torsions fingerprints
    of the molecule.

    The current release of MayaChemTools generates the following types of
    topological atom torsions fingerprints vector strings:

        FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
        3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
        C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
        2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
        2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1

        FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
        3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3
        .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H
        2-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 1 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.B
        O3.H1-O.X1.BO1.H1 1 C.X2.BO2.H2-C.X2.BO2.H2-N.X3.BO3-C.X3.BO4 2 C.X2.B
        O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1...

        FingerprintsVector;TopologicalAtomTorsions:DREIDINGAtomTypes;27;Numeri
        calValues;IDsAndValuesString;C_2-C_3-C_3-C_3 C_2-C_3-C_3-O_3 C_2-C_R-C
        _R-C_3 C_2-C_R-C_R-C_R C_2-C_R-C_R-N_R C_2-N_3-C_R-C_R C_3-C_3-C_2-O_2
        C_3-C_3-C_2-O_3 C_3-C_3-C_3-C_3 C_3-C_3-C_3-N_R C_3-C_3-C_3-O_3 C_...;
        1 1 1 2 1 2 1 1 3 1 3 2 2 2 1 1 1 3 1 2 2 32 2 2 5 3 1

        FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
        lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
        H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
        ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
        4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2

        FingerprintsVector;TopologicalAtomTorsions:FunctionalClassAtomTypes;26
        ;NumericalValues;IDsAndValuesString;Ar-Ar-Ar-Ar Ar-Ar-Ar-Ar.HBA Ar-Ar-
        Ar-HBD Ar-Ar-Ar-Hal Ar-Ar-Ar-None Ar-Ar-Ar.HBA-Ar Ar-Ar-Ar.HBA-None Ar
        -Ar-HBD-None Ar-Ar-None-HBA Ar-Ar-None-HBD Ar-Ar-None-None Ar-Ar.H...;
        32 5 2 2 3 3 3 2 2 2 2 1 2 1 1 1 2 1 1 1 1 3 1 1 1 3

        FingerprintsVector;TopologicalAtomTorsions:MMFF94AtomTypes;43;Numerica
        lValues;IDsAndValuesString;C5A-C5B-C5B-C5A C5A-C5B-C5B-C=ON C5A-C5B-C5
        B-CB C5A-C5B-C=ON-NC=O C5A-C5B-C=ON-O=CN C5A-C5B-CB-CB C5A-CB-CB-CB C5
        A-N5-C5A-C5B C5A-N5-C5A-CB C5A-N5-C5A-CR C5A-N5-CR-CR C5B-C5A-CB-C...;
        1 1 1 1 1 2 2 2 1 1 2 2 2 2 1 1 2 1 1 2 1 2 1 1 1 2 1 1 1 2 18 2 2 1 1
        1 1 2 1 1 3 1 3

        FingerprintsVector;TopologicalAtomTorsions:SLogPAtomTypes;49;Numerical
        Values;IDsAndValuesPairsString;C1-C10-N11-C20 1 C1-C10-N11-C21 1 C1-C1
        1-C21-C21 2 C1-C11-C21-N11 2 C1-CS-C1-C10 1 C1-CS-C1-C5 1 C1-CS-C1-CS
        2 C10-C1-CS-O2 1 C10-N11-C20-C20 2 C10-N11-C21-C11 1 C10-N11-C21-C21 1
        C11-C21-C21-C20 1 C11-C21-C21-C5 1 C11-C21-N11-C20 1 C14-C18-C18-C20
        2 C18-C14-C18-C18 2 C18-C18-C14-F 2 C18-C18-C18-C18 4 C18-C18-C18-C...

        FingerprintsVector;TopologicalAtomTorsions:SYBYLAtomTypes;26;Numerical
        Values;IDsAndValuesPairsString;C.2-C.3-C.3-C.3 1 C.2-C.3-C.3-O.3 1 C.2
        -C.ar-C.ar-C.3 1 C.2-C.ar-C.ar-C.ar 2 C.2-C.ar-C.ar-N.ar 1 C.2-N.am-C.
        ar-C.ar 2 C.3-C.3-C.2-O.co2 2 C.3-C.3-C.3-C.3 3 C.3-C.3-C.3-N.ar 1 C.3
        -C.3-C.3-O.3 3 C.3-C.3-C.ar-C.ar 2 C.3-C.3-C.ar-N.ar 2 C.3-C.3-N.ar-C.
        ar 2 C.3-C.ar-C.ar-C.ar 1 C.3-C.ar-N.ar-C.3 1 C.3-C.ar-N.ar-C.ar 1 ...

        FingerprintsVector;TopologicalAtomTorsions:TPSAAtomTypes;8;NumericalVa
        lues;IDsAndValuesPairsString;N21-None-None-None 9 N7-None-None-None 4
        None-N21-None-None 10 None-N7-None-None 3 None-N7-None-O3 1 None-None-
        None-None 44 None-None-None-O3 3 None-None-None-O4 5

        FingerprintsVector;TopologicalAtomTorsions:UFFAtomTypes;27;NumericalVa
        lues;IDsAndValuesPairsString;C_2-C_3-C_3-C_3 1 C_2-C_3-C_3-O_3 1 C_2-C
        _R-C_R-C_3 1 C_2-C_R-C_R-C_R 2 C_2-C_R-C_R-N_R 1 C_2-N_3-C_R-C_R 2 C_3
        -C_3-C_2-O_2 1 C_3-C_3-C_2-O_3 1 C_3-C_3-C_3-C_3 3 C_3-C_3-C_3-N_R 1 C
        _3-C_3-C_3-O_3 3 C_3-C_3-C_R-C_R 2 C_3-C_3-C_R-N_R 2 C_3-C_3-N_R-C_R 2
         C_3-C_R-C_R-C_R 1 C_3-C_R-N_R-C_3 1 C_3-C_R-N_R-C_R 1 C_3-N_R-C_R-...

  METHODS
    new
            $NewTopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
                                                           %NamesAndValues);

        Using specified *TopologicalAtomTorsionsFingerprints* property names
        and values hash, new method creates a new object and returns a
        reference to newly created TopologicalAtomTorsionsFingerprints
        object. By default, the following properties are initialized:

            Molecule = ''
            Type = 'TopologicalAtomTorsions'
            AtomIdentifierType = ''
            AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC']
            FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']

        Examples:

            $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
                                      'Molecule' => $Molecule,
                                      'AtomIdentifierType' =>
                                                      'AtomicInvariantsAtomTypes');

            $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
                                      'Molecule' => $Molecule,
                                      'AtomIdentifierType' =>
                                                      'AtomicInvariantsAtomTypes',
                                      'AtomicInvariantsToUse' =>
                                                      ['AS', 'X', 'BO', 'H', 'FC'] );

            $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
                                      'Molecule' => $Molecule,
                                      'AtomIdentifierType' =>
                                                      'DREIDINGAtomTypes');

            $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
                                      'Molecule' => $Molecule,
                                      'AtomIdentifierType' =>
                                                      'SYBYLAtomTypes');

            $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
                                      'Molecule' => $Molecule,
                                      'AtomIdentifierType' =>
                                                      'SLogPAtomTypes');

            $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
                                      'Molecule' => $Molecule,
                                      'AtomIdentifierType' =>
                                                      'FunctionalClassAtomTypes',
                                      'FunctionalClassesToUse' =>
                                                      ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] );


            $TopologicalAtomTorsionsFingerprints->GenerateFingerprints();
            print "$TopologicalAtomTorsionsFingerprints\n";

    GetDescription
            $Description = $TopologicalAtomTorsionsFingerprints->GetDescription();

        Returns a string containing description of topological atom torsions
        fingerprints.

    GenerateFingerprints
            $TopologicalAtomTorsionsFingerprints->GenerateFingerprints();

        Generates topological atom torsions fingerprints and returns
        *TopologicalAtomTorsionsFingerprints*.

    GetAtomTorsionsIDs
            $AtomPairIDsRef = $TopologicalAtomTorsionsFingerprints->GetAtomTorsionsIDs();
            @AtomPairIDs = $TopologicalAtomTorsionsFingerprints->GetAtomTorsionsIDs();

        Returns atom torsion IDs corresponding to atom torsion count values
        in topological atom torsions fingerprints vector as an array or
        reference to an array.

    SetAtomIdentifierType
            $TopologicalAtomTorsionsFingerprints->SetAtomIdentifierType($IdentifierType);

        Sets atom *IdentifierType* to use during atom torsions fingerprints
        generation and returns *TopologicalAtomTorsionsFingerprints*.

        Possible values: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes,
        EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
        SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*.

    SetAtomicInvariantsToUse
            $TopologicalAtomTorsionsFingerprints->SetAtomicInvariantsToUse($ValuesRef);
            $TopologicalAtomTorsionsFingerprints->SetAtomicInvariantsToUse(@Values);

        Sets atomic invariants to use during *AtomicInvariantsAtomTypes*
        value of *AtomIdentifierType* for topological atom torsions
        fingerprints generation and returns
        *TopologicalAtomTorsionsFingerprints*.

        Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
        TB, H, Ar, RA, FC, MN, SM*. Default value: *AS,X,BO,H,FC*.

        The atomic invariants abbreviations correspond to:

            AS = Atom symbol corresponding to element symbol

            X<n>   = Number of non-hydrogen atom neighbors or heavy atoms
            BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
            LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
            SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
            DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
            TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
            H<n>   = Number of implicit and explicit hydrogens for atom
            Ar     = Aromatic annotation indicating whether atom is aromatic
            RA     = Ring atom annotation indicating whether atom is a ring
            FC<+n/-n> = Formal charge assigned to atom
            MN<n> = Mass number indicating isotope other than most abundant isotope
            SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
                    3 (triplet)

        Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class
        corresponds to:

            AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>

        Except for AS which is a required atomic invariant in atom types,
        all other atomic invariants are optional. Atom type specification
        doesn't include atomic invariants with zero or undefined values.

        In addition to usage of abbreviations for specifying atomic
        invariants, the following descriptive words are also allowed:

            X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
            BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
            LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
            SB :  NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
            DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
            TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
            H :  NumOfImplicitAndExplicitHydrogens
            Ar : Aromatic
            RA : RingAtom
            FC : FormalCharge
            MN : MassNumber
            SM : SpinMultiplicity

        *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
        atomic invariant atom types.

    SetFunctionalClassesToUse
            $TopologicalTorsionsFingerprints->SetFunctionalClassesToUse($ValuesRef);
            $TopologicalTorsionsFingerprints->SetFunctionalClassesToUse(@Values);

        Sets functional classes invariants to use during
        *FunctionalClassAtomTypes* value of *AtomIdentifierType* for
        topological atom torsions fingerprints generation and returns
        *TopologicalAtomTorsionsFingerprints*.

        Possible values for atom functional classes are: *Ar, CA, H, HBA,
        HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]:
        *HBD,HBA,PI,NI,Ar,Hal*.

        The functional class abbreviations correspond to:

            HBD: HydrogenBondDonor
            HBA: HydrogenBondAcceptor
            PI :  PositivelyIonizable
            NI : NegativelyIonizable
            Ar : Aromatic
            Hal : Halogen
            H : Hydrophobic
            RA : RingAtom
            CA : ChainAtom

         Functional class atom type specification for an atom corresponds to:

            Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None

        *AtomTypes::FunctionalClassAtomTypes* module is used to assign
        functional class atom types. It uses following definitions [ Ref
        60-61, Ref 65-66 ]:

            HydrogenBondDonor: NH, NH2, OH
            HydrogenBondAcceptor: N[!H], O
            PositivelyIonizable: +, NH2
            NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH

    StringifyTopologicalAtomTorsionsFingerprints
            $String = $TopologicalAtomTorsionsFingerprints->
                          StringifyTopologicalAtomTorsionsFingerprints();

        Returns a string containing information about
        *TopologicalAtomTorsionsFingerprints* object.

AUTHOR
    Manish Sud <[e-mail]>

SEE ALSO
    Fingerprints.pm, FingerprintsStringUtil.pm,
    AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm,
    EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm,
    MACCSKeys.pm, PathLengthFingerprints.pm,
    TopologicalAtomPairsFingerprints.pm,
    TopologicalAtomTripletsFingerprints.pm,
    TopologicalPharmacophoreAtomPairsFingerprints.pm,
    TopologicalPharmacophoreAtomTripletsFingerprints.pm

COPYRIGHT
    Copyright (C) 2015 Manish Sud. All rights reserved.

    This file is part of MayaChemTools.

    MayaChemTools is free software; you can redistribute it and/or modify it
    under the terms of the GNU Lesser General Public License as published by
    the Free Software Foundation; either version 3 of the License, or (at
    your option) any later version.